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Release? #306

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merged 84 commits into from
Oct 24, 2024
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15f17ff
added new translation function
BjornFJohansson Mar 27, 2024
d333558
new orfs method for Seq based on three_frame_orfs function
BjornFJohansson Mar 27, 2024
5717dc0
new orfs_to_features method for Dseqrecord
BjornFJohansson Mar 27, 2024
37cbe3e
new extract_from_text functions that also returns the intervening tex…
BjornFJohansson Mar 27, 2024
1fc277d
bugfix orfs for Seq and Dsecrecord
BjornFJohansson Mar 27, 2024
c27e762
added crispr tests
BjornFJohansson Mar 27, 2024
4c4e4cc
added pairwise for older Python versions
BjornFJohansson Mar 27, 2024
f948b8c
older type hint
BjornFJohansson Mar 27, 2024
4d84231
Deploying to gh-pages from @ BjornFJohansson/pydna@da3e7e9cf4b379d15a…
BjornFJohansson Apr 18, 2024
46f9d2c
Deploying to gh-pages from @ BjornFJohansson/pydna@5be4f9db0c36b95839…
BjornFJohansson Apr 18, 2024
64f531b
Deploying to gh-pages from @ BjornFJohansson/pydna@b37a17cc3b5a06aa56…
BjornFJohansson Apr 18, 2024
00795cd
Deploying to gh-pages from @ BjornFJohansson/pydna@11aae3c29bac3dc6da…
BjornFJohansson Apr 18, 2024
d0fef14
Deploying to gh-pages from @ BjornFJohansson/pydna@0f9522372f439d025c…
BjornFJohansson Apr 18, 2024
80834d1
try to build docs locally on gh-pages
BjornFJohansson Apr 18, 2024
806f20e
try to build gh pages
BjornFJohansson Apr 18, 2024
1464e63
try to build gh pages
BjornFJohansson Apr 18, 2024
e13a009
fix
BjornFJohansson Apr 18, 2024
94f6eb0
added sphinx ext
BjornFJohansson Apr 18, 2024
0f947ea
Deploying to gh-pages from @ BjornFJohansson/pydna@bc08a36b1f894780b4…
BjornFJohansson Apr 18, 2024
1c3f678
try fix docs
BjornFJohansson Apr 22, 2024
1864101
build docs
BjornFJohansson Apr 22, 2024
4cfbdb7
clean
BjornFJohansson Apr 22, 2024
255aa46
redirect docs badge to action
BjornFJohansson Apr 22, 2024
96c1de5
redirect docs badge to action
BjornFJohansson Apr 22, 2024
6ddec81
fix readme links
BjornFJohansson Apr 22, 2024
7f013bd
fix readme
BjornFJohansson Apr 22, 2024
23a6a2d
fix
BjornFJohansson Apr 22, 2024
0c43349
try to fix test error
BjornFJohansson Apr 22, 2024
6a72988
fix bug that recognized parts of re enzyme names as other enzymes
BjornFJohansson May 1, 2024
3222075
added comment with number of enzymes
BjornFJohansson May 1, 2024
c61afff
changed number of expected enzymes to the correct number 621
BjornFJohansson May 1, 2024
afac39c
more informative error msg
BjornFJohansson May 1, 2024
444e9fb
closes #216 (2)
manulera Apr 25, 2024
205ed7d
closes #196
manulera May 13, 2024
ac81427
vscode and poetry settings added
manulera May 13, 2024
88c56da
fix test
manulera May 13, 2024
9b8986b
add locations_overlap to utils
manulera Jun 21, 2024
8c1ebb8
Issue 238 (#239)
manulera Jul 15, 2024
2be88fb
closes #240
JeffXiePL Jul 15, 2024
17a1ed1
atomically write default config
jxu10 Mar 29, 2024
2c92f13
optimisation for #237
manulera Jul 16, 2024
47bc08e
fix python 3.8 typing
manulera Jul 16, 2024
d133461
include neb calculator and its tests
manulera Jul 31, 2024
12508a7
fix design and add tests
manulera Jul 31, 2024
019013e
example commit for #176
manulera Aug 12, 2024
3514427
Documentation notebooks 2 (#272)
manulera Sep 30, 2024
31b3322
update contribution guidelines (#274)
manulera Oct 3, 2024
09199a9
update CI action to enforce hooks (#277)
manulera Oct 3, 2024
2cd9d38
update: Added google badge to all notebooks issue #266 (#275)
hiyama341 Oct 3, 2024
1d36eeb
added seguid stamp to Genbank sequence files
BjornFJohansson Oct 3, 2024
610d3f6
fix test sequence file
BjornFJohansson Oct 3, 2024
277f61a
dependabot monthly
BjornFJohansson Oct 3, 2024
26bb292
New CRISPR example notebook (#260) (#284)
hiyama341 Oct 4, 2024
d46b3d9
Updated notebooks (#295)
manulera Oct 7, 2024
03816ec
progress towards #261
manulera Oct 3, 2024
e065db2
WIP
manulera Oct 3, 2024
474a675
remove code image from README for #261
manulera Oct 7, 2024
7e2c247
more README updates + make requirements.txt
manulera Oct 7, 2024
ece5d59
add requirements file
manulera Oct 7, 2024
7464e39
fix configuration
manulera Oct 7, 2024
2b010a9
typing for PrettyTable
Oct 6, 2024
982ceb9
typing for codon dicts
Oct 6, 2024
490f066
typing for Seq
Oct 6, 2024
ae04507
typing for FakeSeq
Oct 6, 2024
e6e1473
typing for Genbank
Oct 6, 2024
a591523
typing for sequence_picker module
Oct 6, 2024
7f89b8c
typing for common_sub_strings module
Oct 6, 2024
b8dbf7b
typing for Assembly.__init__ and Assembly.__repr__
Oct 6, 2024
4b6aa00
Bump pillow from 10.3.0 to 10.4.0
dependabot[bot] Oct 7, 2024
d722b93
Bump autopep8 from 2.1.0 to 2.3.1
dependabot[bot] Oct 7, 2024
ba91fe8
Bump black from 24.4.2 to 24.8.0
dependabot[bot] Oct 7, 2024
cfd1181
Bump sphinx-rtd-theme from 2.0.0 to 3.0.0
dependabot[bot] Oct 7, 2024
959b5d4
Bump prettytable from 3.10.0 to 3.11.0
dependabot[bot] Oct 7, 2024
4c2d929
closes #261 (#297)
manulera Oct 8, 2024
f063c40
tests for #281 #279, add type to pcr (#298)
manulera Oct 8, 2024
fd8577c
update codecov action for #242
manulera Oct 9, 2024
9e86c43
Issue 270 (#301)
manulera Oct 10, 2024
bd8317c
added example.ipynb to tests folder
BjornFJohansson Oct 6, 2024
4340cee
removed example.ipynb
BjornFJohansson Oct 6, 2024
1b142c8
deal with Tm = 0
BjornFJohansson Oct 6, 2024
9d112d7
fix notebook export related to #279
manulera Oct 8, 2024
768c6fa
New docs (#304)
manulera Oct 11, 2024
bca1d08
Fix link in README (#310)
dgruano Oct 15, 2024
72cd39b
Fix action (#311)
manulera Oct 15, 2024
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fix
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BjornFJohansson authored and manulera committed Oct 8, 2024
commit e13a0097e2146b79c076101e50d0d7e3161b030e
2 changes: 1 addition & 1 deletion .github/workflows/publish-docs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ jobs:

- name: Install this Python package
run: |
pip install .[clipboard,download,express,gel]
python -m pip install .[clipboard,download,express,gel]

- name: Session information
run: |
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